Your package structure is broken

Each package structure is sort of broken:

Layered package structure

controller
  file1
  file2
  file3
  …
repos
  file1
  file2
  file3
  …
services
  file1
  file2
  file3
  …

Good: Easy to understand
Bad: Things that belong together are spread all over the project. No true modules.

Module package structure

module1
  FileController
  FileRepo
  FileService
module2
  FileController
  FileRepo
  FileService

Good: True modules
Bad: Layer-Info hard to distinguish, not so easy to understand

Mixed mode

module1
  Controller
    File1
    …
  Repo
    File1
    …
  Service
    File1
    …
module2
  Controller
    File1
    …
  Repo
    File1
    …
  Service
    File1
    …

Good: True modules, Layers easy to spot.
Bad: Mixing of two concepts: Folders for modules, folders for layers. Developers have to travers large dir-structures.

———————
Main problem: You need folder structures to group modules, build modules, show layers. (one concept for different purposes)
Possible solution: Folders for group of modules. (may be nested) Folders with with Manifesto.xml - sorry Manifesto.yml to show module structure to IDE. And „markers“ for layers. (Which are maybe inspected automatically by the IDE.)

What is your favourite? Do you have suggestions?